Tag Archives: Ecological Networks

Ecological networks represent interactions between different biotic units in an ecosystem and are becoming an increasingly popular tool for describing and illustrating a range of different types of ecological interactions. Food webs – which provide a way to track and quantify the flow of energy and resources in ecosystems – are among the most studied type of ecological networks. These networks usually represent species (nodes) which are connected by pairwise interactions (links) and they play a central role in improving our understanding of ecological and evolutionary dynamics.

Historically, food webs described antagonistic relationships (e.g. plant-herbivore or host-parasitoid networks) but the approach has been developed in recent years to include mutualistic networks (e.g. plant-pollinator networks, phorophyte-epiphyte networks). The development of network ecology, including ever more sophisticated methods to analyse ecological communities, has been driven forward by an enthusiastic community of ecologists, theoreticians and modellers working together to enhance our understanding of how communities interact.

In this blog post, we’ll describe the important role played by female scientists in the development of network ecology, focusing on the contributions by two ground-breaking ecologists and also highlighting contributions from a range of other scientists working in this field. Continue reading →

The February issue of Methods is now online! As you may have seen already, it includes the BES cross-journal Special Feature: “Demography Beyond the Population“. There are also eight other wonderful articles to read.

As always, the first issue of the year is our sample issue. You can access all of the articles online free of charge. No subscription or membership is required!

We have two Open Access articles and two Applications papers in our January issue.

– Recognizing False Positives: Environmental DNA (eDNA) is increasingly used for surveillance and detection of species of interest in aquatic and soil samples. A significant risk associated with eDNA methods is potential false-positive results due to laboratory contamination. To minimize and quantify this risk, Chris Wilson et al. designed and validated a set of synthetic oligonucleotides for use as species-specific positive PCR controls for several high-profile aquatic invasive species.

– BiMat: An open-source MATLAB package for the study of the structure of bipartite ecological networks. BiMat enables both multiscale analysis of the structure of a bipartite ecological network – spanning global (i.e. entire network) to local (i.e. module-level) scales – and meta-analyses of many bipartite networks simultaneously. The authors have chosen to make this Applications article Open Access.

Gemma Murray et al. provide this month’s second Open Access article. In ‘The effect of genetic structure on molecular dating and tests for temporal signal‘ the authors use simulated data to investigate the performance of several tests of temporal signal, including some recently suggested modifications. The article shows that all of the standard tests of temporal signal are seriously misleading for data where temporal and genetic structures are confounded (i.e. where closely related sequences are more likely to have been sampled at similar times). This is not an artifact of genetic structure or tree shape per se, and can arise even when sequences have measurably evolved during the sampling period.

As you may know, tomorrow (Saturday 22 August) is National Honey Bee Day in the USA. To mark the day we will be highlighting some of the best papers that have been published on bees and pollinators in Methods in Ecology and Evolution.

You can find out more about National Honey Bee Day (and about bees in general) HERE.

Without further ado though, here are a few of the best Methods papers related to Honey Bees:

Honey Bee Risk Assessment

Our Honey Bee highlights begin with Hendriksma et al.’s article ‘Honey bee risk assessment: new approaches for in vitro larvae rearing and data analyses‘. Robust laboratory methods for assessing adverse effects on honey bee brood are required for research into the issues contributing to global bee losses. To facilitate this, the authors of this article recommend in vitro rearing of larvae and suggest some appropriate statistical tools for the related data analyses. Together these methods can help to improve the quality of environmental risk assessment studies on honey bees and secure honey bee pollination. As this article was published over two years ago, it can be accessed for free by anyone.

This month’s issue contains two Applications article and one Open Access article, all of which are freely available.

– LEA: This R package enables users to run ecological association studies from the R command line. It can perform analyses of population structure and genome scans for adaptive alleles from large genomic data sets. The package derives advantages from R programming functionalities to adjust significance values for multiple testing issues and to visualize results.

–PIPITS: An open-source stand-alone suite of software for automated processing of Illumina MiSeq sequences for fungal community analysis. PIPITS exploits a number of state of the art applications to process paired-end reads from quality filtering to producing OTU abundance tables.

Giovanni Strona and Joseph Veech provide this month’s Open Access article. Many studies have focused on nestedness, a pattern reflecting the tendency of network nodes to share interaction partners, as a method of measuring the structure of ecological networks. In ‘A new measure of ecological network structure based on node overlap and segregation‘ the authors introduce a new statistical procedure to measure both this kind of structure and the opposite one (i.e. species’ tendency against sharing interacting partners).